RFE: custom palettes

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-03-13)
Description
Hi,

I love the availability of the colorbrewer palettes! Would it be possible to add custom defined palettes as well, similarly to how we can have custom colors with the "color name" command? 

Cheers
Oli

Log:
> camera ortho

> lighting soft

> set bgColor white

> lighting depthCueColor white

> cofr centerOfView

UCSF ChimeraX version: 0.9 (2019-03-13)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/Users/oliverclarke/Dropbox/Documents/Work/Projects/RyR/Structures_and_maps/ryr_maps_paper2/paper2_maps/ca30/refine_g_allgood_2_mask_rubi075_f2_b500_r10_goodmics_ct20_post_10_Core.mrc

Opened
refine_g_allgood_2_mask_rubi075_f2_b500_r10_goodmics_ct20_post_10_Core.mrc,
grid size 400,400,400, pixel 1.25, shown at level 0.0284, step 2, values
float32  

> close all

> open 3ch3

3ch3 title:  
Crystal Structure Analysis of SERA5E from plasmodium falciparum [more info...]  
  
Chain information for 3ch3 #1  
---  
Chain | Description  
X | Serine-repeat antigen protein  
  
Non-standard residues in 3ch3 #1  
---  
2HP — dihydrogenphosphate ion  
  
  

> surface #1

> measure convexity #1

Convexity -1.02 - 1.64, mean -0.0435, std deviation 0.362 at 159015 vertices
of 3ch3_X SES surface 1.3  

> select up

Nothing selected  

> measure convexity #1 palette rdylbu-5

Convexity -1.02 - 1.64, mean -0.0435, std deviation 0.362 at 159015 vertices
of 3ch3_X SES surface 1.3  

> measure convexity #1 palette ylgnbu-5

Convexity -1.02 - 1.64, mean -0.0435, std deviation 0.362 at 159015 vertices
of 3ch3_X SES surface 1.3  

> close all

> open /Users/oliverclarke/Dropbox/best_new_4cmc_combined_pixcorr.mrc

Opened best_new_4cmc_combined_pixcorr.mrc, grid size 512,512,512, pixel 1.06,
shown at level 0.0133, step 2, values float32  

> measure convexity #1 palette ylgnbu-5

Convexity -4.85 - 6.28, mean 0.982, std deviation 1.33 at 2122386 vertices of
level 0.01326 1.1  

> surface dust #1 size 20

Unknown command: 100  

> surface dust #1 size 100

> surface dust #1 size 20

> measure convexity #1 palette ylgnbu-5

Convexity -4.42 - 5.05, mean 1.07, std deviation 0.856 at 1432972 vertices of
level 0.01879 1.1  

> set bgColor black

> measure convexity #1 palette ylgnbu-5

Convexity -4.42 - 5.05, mean 1.07, std deviation 0.856 at 1432972 vertices of
level 0.01879 1.1  

> help alias

> toolshed show '"Side View"'

> close all

> open 3ch3

3ch3 title:  
Crystal Structure Analysis of SERA5E from plasmodium falciparum [more info...]  
  
Chain information for 3ch3 #1  
---  
Chain | Description  
X | Serine-repeat antigen protein  
  
Non-standard residues in 3ch3 #1  
---  
2HP — dihydrogenphosphate ion  
  
  

> surface dust #1 size 20

No surfaces specified  

> surface #1

> measure convexity #1 palette ylgnbu-5

Convexity -1.02 - 1.64, mean -0.0435, std deviation 0.362 at 159015 vertices
of 3ch3_X SES surface 1.3  

> measure convexity #1 palette ylgnbu-5 smoothingIterations 10

Convexity -0.901 - 1.09, mean -0.0354, std deviation 0.328 at 159015 vertices
of 3ch3_X SES surface 1.3  

> measure convexity #1 palette ylgnbu-5 smoothingIterations 100

Convexity -0.78 - 0.561, mean -0.0105, std deviation 0.218 at 159015 vertices
of 3ch3_X SES surface 1.3  

> open 1bl8

1bl8 title:  
Potassium channel (KCSA) from streptomyces lividans [more info...]  
  
Chain information for 1bl8 #2  
---  
Chain | Description  
A B C D | protein (potassium channel protein)  
  
  

> close #1

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10

> surface #2

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 50

Convexity -0.555 - 0.612, mean 0.0398, std deviation 0.202 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.593 - 0.674, mean 0.0366, std deviation 0.204 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.577 - 0.64, mean 0.0408, std deviation 0.202 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.624 - 0.635, mean 0.038, std deviation 0.204 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 1

Convexity -1.32 - 2.13, mean -0.00213, std deviation 0.43 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -1.32 - 1.9, mean -0.00612, std deviation 0.435 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -1.37 - 2.16, mean -0.00135, std deviation 0.434 at 67241 vertices
of 1bl8_C SES surface 2.4  
Convexity -1.24 - 1.58, mean -0.00412, std deviation 0.433 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 5

Convexity -0.866 - 1.18, mean 0.00647, std deviation 0.355 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.923 - 1.24, mean 0.0028, std deviation 0.358 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.955 - 1.23, mean 0.0072, std deviation 0.356 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.967 - 1.2, mean 0.00433, std deviation 0.358 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range 1,-1

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range 10,-10

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range 2,-2

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> lighting soft

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range 2,-1

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range 1,-1

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range -1,1

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range -2,2

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range -1.5,1.5

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> set bgColor white

> lighting depthCueColor white

> select up

Nothing selected  

> select up

Nothing selected  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 10 range -1,1

Convexity -0.775 - 1.06, mean 0.0153, std deviation 0.317 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.758 - 1.07, mean 0.0118, std deviation 0.319 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.758 - 1.1, mean 0.0161, std deviation 0.317 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.817 - 1.08, mean 0.0132, std deviation 0.319 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-5 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> hide #!2.1 models

> show #!2.1 models

> hide #!2.2 models

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting gentle

> lighting soft

> lighting full

> show #!2.2 models

> lighting soft

> measure convexity #2 palette blues-5 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylorrd smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylorrd-5 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  
Fetching compressed palette YlOrRd-9 from
http://www.colourlovers.com/api/palettes?keywords=YlOrRd-9&format=json&numResults=100  

> measure convexity #2 palette ylorrd-5 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

Expected a keyword  

> measure convexity #2 palette ylorrd-6 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylorrd-8 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylorrd-3 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette blues-9 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette blues-3 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette blues-5 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-9 smoothingIterations 20 range -1,1

Convexity -0.674 - 0.864, mean 0.0261, std deviation 0.271 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.678 - 0.901, mean 0.0229, std deviation 0.273 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.692 - 0.881, mean 0.027, std deviation 0.271 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.738 - 0.902, mean 0.0243, std deviation 0.273 at 67443 vertices
of 1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-9 smoothingIterations 50 range -1,1

Convexity -0.555 - 0.612, mean 0.0398, std deviation 0.202 at 67402 vertices
of 1bl8_A SES surface 2.2  
Convexity -0.593 - 0.674, mean 0.0366, std deviation 0.204 at 67537 vertices
of 1bl8_B SES surface 2.3  
Convexity -0.577 - 0.64, mean 0.0408, std deviation 0.202 at 67241 vertices of
1bl8_C SES surface 2.4  
Convexity -0.624 - 0.635, mean 0.038, std deviation 0.204 at 67443 vertices of
1bl8_D SES surface 2.5  

> measure convexity #2 palette ylgnbu-9 smoothingIterations 40 range -1,1

Convexity -0.59 - 0.674, mean 0.0367, std deviation 0.219 at 67402 vertices of
1bl8_A SES surface 2.2  
Convexity -0.62 - 0.733, mean 0.0335, std deviation 0.222 at 67537 vertices of
1bl8_B SES surface 2.3  
Convexity -0.603 - 0.699, mean 0.0377, std deviation 0.219 at 67241 vertices
of 1bl8_C SES surface 2.4  
Convexity -0.653 - 0.702, mean 0.035, std deviation 0.221 at 67443 vertices of
1bl8_D SES surface 2.5  

> lighting full

> close all

> open 1bl8

1bl8 title:  
Potassium channel (KCSA) from streptomyces lividans [more info...]  
  
Chain information for 1bl8 #1  
---  
Chain | Description  
A B C D | protein (potassium channel protein)  
  
  

> rainbow palette rdylbu-9




OpenGL version: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tom Goddard]

Another request made for this feature #4419